Multiplex primer prediction software for divergent targets

Gardner, Shea N.; Hiddessen, Amy L.; Williams, Peter L.; Hara, Christine; Wagner, Mark C.; Colston, Bill W.

The software handles a large number of input sequences, although for very diverse targets the predicted primer multiplex may be too large to be empirically feasible. For many target sets, such as those including all the genomes of a species, predicting a universal primer set requires only minutes up to a few hours, although for inputs with thousands of sequences a run may take days. We used MPP to design a universal primer set for a target set of all virus genomes, and showed that even if short primers are used, thousands of priming sequences would be required to amplify all sequenced viruses. We then applied MPP to design multiplex family level primers for every viral family, as well as for some diverse species target sets too large for other available primer prediction software.